Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 3RLE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.9 22.3 - - + +
8A GLU 3.5 25.1 - - - +
9A ILE* 4.1 12.8 - - + -
10A PRO* 3.8 19.1 - - + -
41A VAL* 4.2 6.1 - - + -
70A LEU* 4.1 23.6 - - + -
71A ILE 3.1 18.2 - - - +
72A TYR* 3.9 19.3 - - + -
78A GLU* 1.3 84.7 - - - +
80A ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA 5.1 2.0 + - - -
32A GLY 3.0 24.9 + - - -
33A LEU* 4.2 4.9 - - - +
34A GLU* 4.6 5.8 + - - +
38A ASP* 2.7 42.4 + - - -
69A MSE 3.6 0.7 - - - +
70A LEU* 3.4 5.3 - - - +
71A ILE* 2.8 62.3 + - + +
73A SER* 4.0 12.7 - - - +
78A GLU 5.6 0.4 + - - -
79A LEU* 1.3 76.4 - - - +
81A GLU* 1.3 72.6 + - - +
82A THR* 4.9 8.4 - - - +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 3.2 45.7 + - + +
69A MSE 3.2 7.6 - - - +
70A LEU* 3.7 27.3 - - + +
80A ARG* 1.3 77.3 - - - +
82A THR* 1.3 62.9 + - - +
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 2.8 30.1 + - + +
33A LEU* 4.7 4.0 - - + -
67A VAL 3.7 0.2 - - - +
68A LYS* 3.7 3.8 - - - -
69A MSE 2.8 48.9 + - + +
71A ILE* 4.1 23.3 - - + -
80A ARG* 4.9 11.2 - - - +
81A GLU* 1.3 75.7 - - - +
83A SER* 1.3 67.7 + - - +
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.3 19.6 - - - +
66A PRO* 3.6 24.8 - - - +
67A VAL 3.3 8.8 + - - -
68A LYS* 4.5 3.1 - - - +
82A THR* 1.3 78.4 + - - +
84A VAL* 1.3 63.0 + - - +
85A THR* 5.1 0.7 + - - -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO* 3.5 34.8 - - + +
28A GLY* 4.1 1.3 - - - +
31A ALA* 3.8 3.8 - - + -
59A LEU* 5.3 1.8 - - + -
66A PRO* 4.3 0.7 - - - -
67A VAL* 2.7 51.2 + - + +
69A MSE 3.1 36.8 - - + -
83A SER* 1.3 73.7 + - - +
85A THR* 1.3 65.6 + - - +
86A PRO* 3.3 5.1 - - + +
96A LEU* 3.7 31.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il